How to get started with micromamba on HPC
This guide explains how to install micromamba, recreate a shared environment, and use it on a Slurm-based HPC cluster
1. Install Micromamba
Micromamba is a lightweight, standalone conda package manager—ideal for HPC systems.
Quick Install
# create a directory for micromamba
mkdir -p ~/micromamba # change this path as needed
# Download and install micromamba to ~/micromamba
curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj -C ~/micromamba
# Add installation to your shell config (~/.bashrc)
./micromamba/bin/micromamba shell init -s bash -r ~/micromamba # this writes to your .bashrc file
# then restart your terminal!Verify Installation
micromamba --version3. Verify the enviroment installation
Once the installation is complete, you can verify it by activating the environment and checking the installed packages:
micromamba activate my_env_name # replace with your environment nameThis will download and install all packages specified in the environment file.